Lampreys, also known as kanakana, are found in Otago's coastal waters too, but the Department of Conservation and Otago Fish and Game had not heard of any similar issues in the region.
The fish in the Mataura River appeared to have red-coloured fins and red contusions (pictured), which were first noticed by Hokonui Runanga chairman and kaumatua Rewi Anglem.
Aquatic scientist Andy Hicks said fresh samples were collected on Wednesday and sent to the Ministry of Agriculture and Forestry to test for pathogens.
As it was not known what caused the contusions, people were advised not to eat fish that did not appear to be completely healthy.
Also, if anyone saw fish with the marks, they should contact Environment Southland, he said.
No problems had been reported from another lamprey-harvesting area on the Waikawa River.
Public Health South had been advised.
